Annotate cells online

1:boot Model Whole (level1) B_mature (level2) Dendritic_classical (level2) Ductal (level2) Endothelial (level2) Fibroblast (level2) Macrophage (level2) Monocyte (level2) Mural (level2) Squamous (level2) T&NK (level2) Safe mode 2:load file 3:run

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Download pred.csv

This page conducts cell annotations on the uploaded gene expression files

1. Input file configuration
   • Should contain gene expression matrix (cell_barcode × gene_id)
   • Raw expression must be 1e4-normalized & log1p-transformed
     normalized up to 10,000 counts per cell, then log-transformed with 1 pseudocount
   • File format: .csv or .csv.gz
2. Cell annotation
   • Performed per cell barcode with a selectable model
   • PANGEA provides one Level1 model and ten Level2 models
   • Level1: 32 cell types; Level2 (combined): 165 annotations
   • Predictions are based on pre-trained logistic regression models
   • Results may differ from the original PANGEApy package (github.com/srkim727/pangeapy)
3. Output file configuration
   • Output file: pred.csv with three columns for each cell barcode
   • predicted_label – predicted cell label from the selected model
   • conf_score – confidence score from the model prediction
   • cert_score – certainty compared to other labels within the model

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